identifier: METPO:1000602
label: aerobic
definition: An oxygen preference in which growth occurs in the presence of molecular
  oxygen (O₂), typically using O₂ as the terminal electron acceptor.
definition_source: PMID:21413255
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000601
synonyms:
- synonym_text: Ox_aerobic
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: aerobe
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: PMID:21413255
  snippet: aerobes require molecular oxygen as a terminal electron acceptor
  notes: Supports aerobic growth as oxygen-dependent respiration.
- reference: PMID:21183663
  snippet: Bacillus subtilis is an aerobic spore-forming Gram-positive bacterium
  notes: 'Organism example: Bacillus subtilis is described as aerobic.'
canonical_examples:
- taxon_id: NCBITaxon:287
  taxon_label: Pseudomonas aeruginosa
  note: "obligate aerobe (respiratory metabolism)"
  reference: PMID:31597590
- taxon_id: NCBITaxon:1270
  taxon_label: Micrococcus luteus
  note: "strict aerobe"
  reference: PMID:19948807
causal_graphs:
- graph_id: aerobic_trait_mechanism
  title: Aerobic growth oxygen-use mechanism
  description: Evidence-backed causal sketch linking the aerobic trait to oxygen-dependent
    respiration.
  nodes:
  - node_id: aerobic_trait
    label: aerobic
    node_type: TRAIT
    grounding: METPO:1000602
    description: Growth occurs in the presence of molecular oxygen.
  - node_id: aerobic_respiration
    label: aerobic respiration
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0009060
    description: Energy release process requiring oxygen as terminal electron acceptor.
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Dioxygen used by aerobes as terminal electron acceptor.
  - node_id: terminal_electron_acceptor
    label: terminal electron acceptor
    node_type: MOLECULAR_FUNCTION
    description: Functional role played by oxygen in aerobic respiration.
    grounding: METPO:1007504
  - node_id: substrate_dehydrogenases
    label: substrate dehydrogenases
    node_type: GENE_OR_PROTEIN
    description: Dehydrogenases (e.g. NADH dehydrogenases) that feed electrons into
      the respiratory chain.
  - node_id: quinone_pool
    label: quinone pool
    node_type: CHEMICAL
    description: Membrane quinone pool (ubiquinone/menaquinone) carrying electrons
      in the respiratory chain.
  - node_id: terminal_oxidases
    label: terminal oxidases
    node_type: GENE_OR_PROTEIN
    description: Respiratory quinol/cytochrome oxidases that reduce O2 to water as
      the final ETC step.
  - node_id: proton_motive_force
    label: proton motive force
    node_type: BIOLOGICAL_PROCESS
    description: Transmembrane electrochemical gradient generated by respiration that
      drives ATP synthesis.
  - node_id: atp_synthesis
    label: ATP synthesis
    node_type: BIOLOGICAL_PROCESS
    description: Energy conservation by ATP synthase powered by the proton motive
      force.
    grounding: GO:0006754
  - node_id: reactive_oxygen_species
    label: reactive oxygen species
    node_type: CHEMICAL
    description: Superoxide, hydrogen peroxide and related species formed endogenously
      during aerobic respiration.
    grounding: CHEBI:26523
  - node_id: ros_scavenging_enzymes
    label: ROS-scavenging enzymes
    node_type: GENE_OR_PROTEIN
    description: Superoxide dismutases, catalases and peroxidases that detoxify reactive
      oxygen species.
  edges:
  - subject: aerobic_trait
    predicate: depends on
    object: molecular_oxygen
    description: Aerobic growth depends on molecular oxygen availability.
    evidence:
    - reference: DOI:10.1016/j.celrep.2023.112444
      snippet: obligate aerobe ... exposed to hypoxia, stops growing
      notes: Mycobacterium tuberculosis example supports oxygen dependence for aerobic
        growth.
    predicate_id: RO:0002502
  - subject: aerobic_trait
    predicate: has mechanistic process
    object: aerobic_respiration
    description: The aerobic trait is mechanistically tied to oxygen-dependent respiration.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2011.06.016
      snippet: respiratory quinol:O2 oxidoreductase
      notes: Review supports oxygen-reducing terminal oxidases as core aerobic respiratory
        enzymes.
  - subject: aerobic_respiration
    predicate: depends on
    object: molecular_oxygen
    description: Aerobic respiration requires oxygen.
    evidence:
    - reference: DOI:10.1016/j.celrep.2023.112444
      snippet: transfer electrons from the ETC to O2
      notes: Supports molecular oxygen as the terminal acceptor for bacterial respiratory
        electron transport.
    predicate_id: RO:0002502
  - subject: molecular_oxygen
    predicate: acts as
    object: terminal_electron_acceptor
    description: In aerobic energy metabolism, molecular oxygen acts as the terminal
      electron acceptor.
    evidence:
    - reference: DOI:10.1016/j.celrep.2023.112444
      snippet: terminal oxidases transfer electrons from the ETC to O2
      notes: Supports oxygen's electron-acceptor role in terminal oxidase activity.
  - subject: substrate_dehydrogenases
    predicate: transfers electrons to
    object: quinone_pool
    description: Substrate dehydrogenases pass electrons to the membrane quinone pool
      in the respiratory chain.
    evidence:
    - reference: DOI:10.1128/ecosalplus.esp-0012-2015
      notes: Electrons are transferred from substrate-specific dehydrogenases to a
        quinone pool (menaquinone, ubiquinone, dimethylmenaquinone).
    predicate_id: METPO:2007403
  - subject: quinone_pool
    predicate: transfers electrons to
    object: terminal_oxidases
    description: Reduced quinol is oxidized by terminal oxidases that reduce O2 to
      water.
    evidence:
    - reference: DOI:10.1128/ecosalplus.esp-0012-2015
      notes: Quinol-to-O2 oxidation is catalyzed by quinol oxidases (cytochrome bo3,
        cytochrome bd) reducing O2 to H2O.
    predicate_id: METPO:2007403
  - subject: terminal_oxidases
    predicate: reduces
    object: molecular_oxygen
    description: Terminal oxidases catalyze the four-electron reduction of O2 to water.
    evidence:
    - reference: DOI:10.3390/antiox13030383
      notes: Terminal oxidases catalyze the four-electron reduction of O2 to water
        and generate the proton motive force for ATP.
    predicate_id: METPO:2000017
  - subject: terminal_oxidases
    predicate: generates
    object: proton_motive_force
    description: Respiratory terminal oxidases generate the proton motive force.
    evidence:
    - reference: DOI:10.3390/antiox13030383
      notes: Terminal oxidases catalyze reduction of O2 to water and generate the
        proton motive force for ATP.
    predicate_id: biolink:produces
  - subject: proton_motive_force
    predicate: powers
    object: atp_synthesis
    description: The transmembrane electrochemical gradient powers ATP synthesis.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      notes: The transmembrane electrochemical gradient powers the membrane proteins
        that synthesize ATP.
  - subject: aerobic_respiration
    predicate: generates
    object: reactive_oxygen_species
    description: Aerobic respiration produces ROS endogenously via respiratory flavoproteins.
    evidence:
    - reference: DOI:10.30970/sbi.1702.716
      notes: ROS are formed endogenously during aerobic respiration due to activity
        of respiratory flavoproteins.
    predicate_id: biolink:produces
  - subject: ros_scavenging_enzymes
    predicate: detoxifies
    object: reactive_oxygen_species
    description: SODs, catalases and peroxidases eliminate reactive oxygen species,
      enabling aerobic growth.
    evidence:
    - reference: DOI:10.30970/sbi.1702.716
      notes: 'Elimination of radicals via ROS-scavenging enzymes: superoxide dismutases
        (SODs), catalases and peroxidases.'
curation_history:
- timestamp: '2026-05-05T01:35:46.849227+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-05T01:09:05-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Added definition source and evidence for oxygen-dependent aerobic growth.
  llm_assisted: true
- timestamp: '2026-05-05T18:39:46-07:00'
  curator: codex
  action: ADDED_ORGANISM_EXAMPLE
  changes: Added Bacillus subtilis organism example with PMID-backed evidence.
  llm_assisted: true
- timestamp: '2026-05-07T00:00:00-07:00'
  curator: codex
  action: ADDED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph for oxygen-dependent aerobic respiration.
  llm_assisted: true
- timestamp: '2026-05-10T00:00:00-07:00'
  curator: codex
  action: IMPROVED_CAUSAL_GRAPH_EVIDENCE
  changes: Added DOI-backed edge evidence to the aerobic respiration causal graph.
  llm_assisted: true
- timestamp: '2026-05-13T22:45:00-07:00'
  curator: codex
  action: IMPROVED_CAUSAL_GRAPH_EVIDENCE
  changes: Removed PMID and GO fallback references from CausalEdge evidence where
    DOI-backed evidence already supported the same oxygen-use mechanisms.
  llm_assisted: true
- timestamp: '2026-05-24T04:41:03Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007504×1).
  llm_assisted: true
- timestamp: '2026-05-26T05:00:47Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings:
    requires → depends on ×2.'
  llm_assisted: true
- timestamp: '2026-05-26T05:00:49Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002502×2).
  llm_assisted: true
- timestamp: '2026-06-17T04:09:43Z'
  curator: claude
  action: REMOVE_REDUNDANT_SYNONYM
  changes: Removed 1 synonym(s) whose text duplicated the label (seeder redundancy;
    no information lost).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 7 evidence-backed generic edges (7 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:09Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007403×2, biolink:produces×2, METPO:2000017×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:30Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0006754×1, CHEBI:26523×1).
  llm_assisted: true